The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- #406 - Updating modules and removing warnings before release 1.3.0 (@danilodileo)
- #405 - Upgrade EUKulele to 2.1.2. This appears to fix problems with downloads of certain databases (@erikrikarddaniel)
- #404 - Added new reference for SPAdes in CITATIONS.md (@danilodileo)
- #394 - allow unzipped input files (@erikrikarddaniel)
- #389 - template update to nf-core tools 3.3.2 plus module updates (@erikrikarddaniel)
- #402 - improve documentation for download of FigShare Diamond files (@erikrikarddaniel)
- #402 - allow the BBNorm process to only use 0.8 of the allocated memory not to fail on oversubscription of memory (@erikrikarddaniel)
- #400 - fix problems with
COLLECT_STATSwhen single end reads are used; closes #396 (@erikrikarddaniel) - #398 - make sure the EUKulele database directory is created if it doesn't exist (@erikrikarddaniel)
- #391,#392 - update the documentation and fix some inconsistencies in which output files are saved (@erikrikarddaniel)
- #390 - remove resource limits on full scale AWS tests to make it work (@erikrikarddaniel)
- #373 - Add module to save tsv with unique ORF Kofamscan hits to
<outdir>/summary_tables(@erikrikarddaniel) - #366 - Save amino acid sequences for HMMER hits (@erikrikarddaniel)
- #368 - Added eukulele database name in filenames (@m3hdad)
- #367 - Gzip Transdecoder output (@erikrikarddaniel)
- #359 - Updated some descriptions and error messages in the json schema for better readability. Also made the input validation stricter in the hopes of preventing more errors during the pipeline run. (@herich0)
- #352 - Updated some modules (@erikrikarddaniel)
- #380 - Fix malformatted versions in two modules (@erikrikarddaniel)
- #378 - Add more nf-test tests (@erikrikarddaniel)
- #377 - Updated default nf-test (@erikrikarddaniel)
- #376 - Template update to nf-core tools 3.3.1 (@erikrikarddaniel)
- #372 - Fix bug in overall stats table creation for certain sample names (@erikrikarddaniel)
- #371 - Template update to nf-core tools 3.2.1 (@erikrikarddaniel)
- #363 - Handle duplicate names in taxonomies better (@erikrikarddaniel)
- #362 - Ensure correct Transdecoder publishing and test assertions (@m3hdad)
- #361 - Ensure
COLLECT_STATSexecutes properly when trimming is skipped (@m3hdad).
- #364 - Use
wgetnotgnu-wgetto fetch KofamScan database to improve arm64 support (@dslarm) - #352 - Updated some modules (@erikrikarddaniel).
- #352 - Assign less memory to BBNorm to avoid getting killed (@erikrikarddaniel).
- #331 - Added nf-tests.
- #320 - added taxonomy directly with Diamond, part 2
- #312 - added taxonomy directly with Diamond, see
--diamond_dbs. - #286 - added an option to save the fasta file output from formatspades.nf module.
- #285 - added nf-test for default settings.
- #280 - Added minid option to bbmap_align module. Now the threshold for mapping a read to a contig is an identity of 0.9. The previous version of nf-core/metatdenovo used the default for BBMap, 0.76. This version might hence give slightly different results than the previous.
- #271 - Added flavor to SPADES modules.
- #332 - Rearranged tree structure for local modules and local subworkflows.
- #330 - Update Usage.md.
- #326 - Clean up overall stats table.
- #323 - Modified param names for input of assembly and ORFs; added name params for output file naming.
- #323 - Removed default for
assemblerandorf_callerparameters. - #318 - Template 3.2.0 update.
- #311 - Update modules and subworkflows.
- #295 - Update documentation.
- #292 - Specify memory to Megahit process.
- #290 - Template update to v2.14.1.
- #283 - Updated documentation about download databases manually.
- #268 - Don't save so many intermediate Megahit files by default.
- #328 - Fix BBDuk was passing only one sample.
- #326 - Fix resources for test cases.
- #326 - Fix output file names for Eukulele and Kofamscan.
- #321 - Fix how params.sequence_filter was called in BBDuk module.
- #305 - Make EUKulele counts output optional as it's not always created.
- #269 - Make Transdecoder work better with
-resume.
- #277 - Fix mistake in how
--eukulele_dbparameter is handled. Remove possibility to use a list of dbs in the same run. - #277 - Gzip user provided assembly files to avoid overwriting by assuming they're already zipped.
Initial release of nf-core/metatdenovo, created with the nf-core template.